Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A24 F31 I2 R1 18 53.0 1873152 93.2% 1745777 143.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913_3_pae_tpiA 1,544,022 1 bp→AA coding (39/1389 nt) narU ← nitrate/nitrite transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_pae_tpiA1,544,0211.A77.8% 122.7 / 30.6 45coding (40/1389 nt)narUnitrate/nitrite transporter
Reads supporting (aligned to +/- strand):  ref base . (6/4);  new base A (14/21);  total (20/25)
Fisher's exact test for biased strand distribution p-value = 3.01e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
*NC_000913_3_pae_tpiA1,544,0220CA100.0% 145.7 / NA 45L13F (TTG→TTT) narUnitrate/nitrite transporter
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (20/25);  total (20/25)

TGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CG‑C‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGAAAG  >  NC_000913_3_pae_tpiA/1543896‑1544171
                                                                                                                                |||                                                                                                                                                    
tGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGCCTATTTTtc                                                                                                                                  >  1:63864/1‑149 (MQ=255)
          atcATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCa                                                                                                                        <  1:491178/147‑1 (MQ=255)
             aTCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTg                                                                                                                     >  1:369810/1‑149 (MQ=255)
                  gACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCata                                                                                                                <  1:741150/149‑1 (MQ=255)
                       aGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCCA‑A‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCCTATtttt                                                                                                           >  2:26673/1‑149 (MQ=255)
                        cgatctaagaagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTc                                                                                                          <  1:839353/143‑1 (MQ=255)
                          aGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATCTGTTTTTCTTTATTTTCCCAGATGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCt                                                                                                        <  2:774770/149‑1 (MQ=255)
                            gCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CG‑AAAAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGttacaca                                                                                                      >  1:424801/1‑144 (MQ=255)
                            gCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CG‑AAAAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTca                                                                                                      >  1:589585/1‑149 (MQ=255)
                             cAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTaac                                                                                                     >  1:546474/1‑149 (MQ=255)
                               agaagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTTTTTTTTTTCTGTGCCATATTGTTccagttcg                                                                                                   >  2:839353/1‑143 (MQ=255)
                               agaagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACAt                                                                                                   <  1:194483/149‑1 (MQ=255)
                                   gTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGcac                                                                                               >  2:286904/1‑149 (MQ=255)
                                      gACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGcacaca                                                                                            >  1:189166/1‑149 (MQ=255)
                                       aCAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CG‑AAAAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCGCATGCACACAt                                                                                           >  1:667218/1‑149 (MQ=255)
                                       aCAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCAAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGcaaccat                                                                                           >  2:550869/1‑144 (MQ=255)
                                         acctgactgaTATCCAGAGATTTCTTCGAGCAATATGTTATCCCGCATGTTTCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTg                                                                                         <  1:875612/147‑1 (MQ=255)
                                         aaCTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTTTCATTTTGCAGTGCCATATTGTTCCTCACATTCACACATTg                                                                                         >  2:173810/1‑149 (MQ=255)
                                         aaCTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTg                                                                                         <  1:930824/149‑1 (MQ=255)
                                              actgaTACCGGGAGATTTCTTCGCGCAATATGTTTTCCTTTATTTTCCCAGGAGGCCGGATTTTCTGGTTTAAAAAAA‑CAAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAAt                                                                                    <  2:590563/149‑1 (MQ=255)
                                               ctgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CG‑AAAAAAGATAACGACTATTTTTCTCATTTTGCAATGCCATATTGTTCCTAACATGCACCCATTGGTAAtt                                                                                   >  1:394780/1‑148 (MQ=255)
                                                      ccAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGaaaaaaa                                                                            <  2:189166/149‑1 (MQ=255)
                                                      ccAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCACATTGTTCCTCACATGCACACATTGGTAATGaaaaaaa                                                                            <  2:911499/149‑1 (MQ=255)
                                                        agagATTTCTTCGAGCAATATTTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGa                                                                          <  1:611578/149‑1 (MQ=255)
                                                               tcttcGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CG‑AAAAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAaca                                                                   <  1:431686/149‑1 (MQ=255)
                                                                 ttcGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CG‑AAAAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACg                                                                 >  2:3027/1‑149 (MQ=255)
                                                                   cGAGCTATATGTGTTCCTTTATTTTCTCAGAAGGCCGGATGTTCTGGTTTCCAGTCG‑TGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCAAATTGTTCCTCCTGACGACACCTTGGTCATTAAAAAAAGACAAAGCACGAg                                                               <  2:160860/149‑1 (MQ=255)
                                                                   cGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAg                                                               <  2:589585/149‑1 (MQ=255)
                                                                   cGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAg                                                               <  1:675148/149‑1 (MQ=255)
                                                                     aGCAATATGTTTTCCTGTATTGTCCCCGAAGGCCGGATTTTCTGGTTGCCAGTCG‑CGAA‑AAAAGCTAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTTACATGCAAACATAAATGCTGAAAAAAACACCCACCGCGAGGt                                                             <  2:907650/149‑1 (MQ=255)
                                                                          tatGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACAAGGTAAGgc                                                        <  1:772732/149‑1 (MQ=255)
                                                                              ttttCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CG‑AAAAAATATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCaa                                                    <  2:298464/149‑1 (MQ=255)
                                                                                    tttATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCatat                                                                                                               <  1:339974/84‑1 (MQ=255)
                                                                                    tttATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCatat                                                                                                               >  2:339974/1‑84 (MQ=255)
                                                                                    tttATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGcac                                                                                               >  2:597368/1‑100 (MQ=255)
                                                                                    tttATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CG‑AAAAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGcac                                                                                               <  1:597368/100‑1 (MQ=255)
                                                                                    tttATTTTCCCAGAAGGCCGGATTTTCTGGTGTCCAGGCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGGGGAAAGGCGCAATAGCCa                                              >  2:925513/1‑149 (MQ=255)
                                                                                           tCCCAGCAGGCCGGATTTGCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGATGTAAGGCGCAATAGCCAGttatta                                       <  1:108979/149‑1 (MQ=255)
                                                                                                   ggCCGGATTTTCGGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAg                               <  2:73948/149‑1 (MQ=255)
                                                                                                   gcccGGATTTTCTGGTTTACAGTCG‑CGAA‑AAAAGAGAACGAATATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAg                               <  2:625027/147‑1 (MQ=255)
                                                                                                    gCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAgg                              >  1:248564/1‑149 (MQ=255)
                                                                                                     ccGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGa                             <  1:759720/149‑1 (MQ=255)
                                                                                                        gATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTTATTTTTCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGGATTAAGGATGa                          >  2:513134/1‑149 (MQ=255)
                                                                                                             tCTGGTTTCCATGCG‑CG‑AAAAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTgg                     <  1:365458/149‑1 (MQ=255)
                                                                                                                    tCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGt              >  1:64411/1‑149 (MQ=255)
                                                                                                                             gcgaaaaaaGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATTGCCTGGTAGTAGAATGAAGGATGAATTGGGTGAAGTGCTGAtt       >  1:259246/6‑149 (MQ=255)
                                                                                                                             gcgaaaaaaGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGACTTGGGTGAAGTGCTGAtt       >  2:911591/6‑149 (MQ=255)
                                                                                                                               gaaaaaaGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGa     >  1:849710/4‑149 (MQ=255)
                                                                                                                                 aaaaaGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGaaa   <  1:286904/148‑1 (MQ=255)
                                                                                                                                 aaaaaGATAACGACTATTTTTCTCATGTTGCAGTGCCATATTGTTCCTCACATGCTCACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGaaa   <  1:26673/148‑1 (MQ=255)
                                                                                                                                 aaaaaGAGAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGaaa   <  2:248564/148‑1 (MQ=255)
                                                                                                                                  aaaaGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGAAAg  >  2:701735/1‑149 (MQ=255)
                                                                                                                                |||                                                                                                                                                    
TGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CG‑C‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGAAAG  >  NC_000913_3_pae_tpiA/1543896‑1544171

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A